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I think it's more of a convention than a rule of logic. That said, there are compelling reasons why this is the case.

Mostly, it's to address the imbalance that would be created if, in heads-up play, the button was also the Big Blind (BB). Here are my thoughts:

If you give the BB the button, then they act last pre-flop and post-flop. Acting last is one of the most influential advantages in poker. Allowing one player to control that influence for the duration of one hand, disincentivizes the Small Blind (SB) to play at all.

As the cost of the BB is greater pre-flop, this is a positive incentive to play as the price of entry into a hand is reduced. Another disincentive for the SB to contest a hand.

Overall, although both players most likely see both scenarios with equal frequency, strategic elements of gameplay are diminished due to the theoretical advantages the BB would gain from being the Button, acting last pre-flop and post-flop. That doesn't really benefit anyone, not even the house/casino as they mostly only rake hands that see flops.

Good answer. Do you have any additional thoughts on why it's not profitable to min-raise as the button 100% of the time? Naively, it seems optimal; you are pretending you are the big blind while being the button, and that you are playing for double the stakes. When you are not the big blind and your opponent folds instead of raising, you win a little extra than you would if he was naturally the big blind for double.
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Cory KendallJan 6 '13 at 3:24

@CoryKendall Min-raising from the BTN 100% could certainly be profitable. It depends on the game dynamics. The depth of the stacks and SPR in play though would seem to me the most influential factors aside from strategy. The deeper the stacks, the less advantage position has.
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Toby Booth♦Jan 6 '13 at 4:16